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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ) $local_species = 'aar' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ) $local_species = 'aar' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ) $local_species = 'amhyb' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ) $local_species = 'amhyb' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ) $local_species = 'atr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ) $local_species = 'atr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ) $local_species = 'aly' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ) $local_species = 'aly' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ) $local_species = 'ath' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ) $local_species = 'ath' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ) $local_species = 'arhy' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ) $local_species = 'arhy' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ) $local_species = 'ama' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ) $local_species = 'ama' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ) $local_species = 'bvu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ) $local_species = 'bvu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ) $local_species = 'bca' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ) $local_species = 'bca' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ) $local_species = 'bna' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ) $local_species = 'bna' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ) $local_species = 'bol' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ) $local_species = 'bol' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ) $local_species = 'bra' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ) $local_species = 'bra' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ) $local_species = 'camsi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ) $local_species = 'camsi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ) $local_species = 'cansat' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ) $local_species = 'cansat' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ) $local_species = 'cru' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ) $local_species = 'cru' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ) $local_species = 'can' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ) $local_species = 'can' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ) $local_species = 'chi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ) $local_species = 'chi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ) $local_species = 'cpa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ) $local_species = 'cpa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ) $local_species = 'ccl' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ) $local_species = 'ccl' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ) $local_species = 'cav' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ) $local_species = 'cav' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ) $local_species = 'dca' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ) $local_species = 'dca' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ) $local_species = 'dzi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ) $local_species = 'dzi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ) $local_species = 'eca' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ) $local_species = 'eca' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ) $local_species = 'esa' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ) $local_species = 'esa' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ) $local_species = 'fve' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ) $local_species = 'fve' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ) $local_species = 'fan' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ) $local_species = 'fan' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ) $local_species = 'gma' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ) $local_species = 'gma' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ) $local_species = 'ghi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ) $local_species = 'ghi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ) $local_species = 'lja' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ) $local_species = 'lja' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ) $local_species = 'lal' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ) $local_species = 'lal' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ) $local_species = 'mbi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ) $local_species = 'mbi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ) $local_species = 'mdo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ) $local_species = 'mdo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ) $local_species = 'pso' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ) $local_species = 'pso' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ) $local_species = 'pvu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ) $local_species = 'pvu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ) $local_species = 'ptr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ) $local_species = 'ptr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ) $local_species = 'rch' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ) $local_species = 'rch' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ) $local_species = 'sbr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ) $local_species = 'sbr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ) $local_species = 'sci' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ) $local_species = 'sci' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ) $local_species = 'sly' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ) $local_species = 'sly' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ) $local_species = 'tpr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ) $local_species = 'tpr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ) $local_species = 'twi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ) $local_species = 'twi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $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' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ) $local_species = 'vmu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ), 'gf_id' => 'HOM05D001286', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001286' ), 'data_identifier' => 'HOM05D001286', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001286', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '487', 'num_species' => '81' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p28080' => 'bna', 'A02p11260' => 'bna', 'A02p25680' => 'bna', 'A02p26050' => 'bna', 'A02p26080' => 'bna', 'A02p26090' => 'bna', 'A03p29440' => 'bna', 'A03p29650' => 'bna', 'A03p29660' => 'bna', 'A07p01550' => 'bna', 'A07p16390' => 'bna', 'A09p10830' => 'bna', 'A09p10860' => 'bna', 'A09p26900' => 'bna', 'A09p26950' => 'bna', 'A10p04770' => 'bna', 'A10p04790' => 'bna', 'A10p32250' => 'bna', 'Aa31csc81G80' => 'aar', 'Aa31LG2G11100' => 'aar', 'Aa31LG2G11120' => 'aar', 'Aa31LG2G11150' => 'aar', 'Aa31LG5G23940' => 'aar', 'Aa31LG5G23960' => 'aar', 'Aa31LG5G24010' => 'aar', 'Actinidia05421' => 'ach', 'Actinidia23609' => 'ach', 'Ah.08g210520' => 'amhyb', 'Ah.15g090840' => 'amhyb', 'AL2G18850' => 'aly', 'AL3G32070' => 'aly', 'AL4G43800' => 'aly', 'AL5G37800' => 'aly', 'AL6G43900' => 'aly', 'AL6G44750' => 'aly', 'AL6G47230' => 'aly', 'AL6G47240' => 'aly', 'Aqoxy2G02367' => 'aox', 'Aqoxy2G03007' => 'aox', 'Aqoxy2G03009' => 'aox', 'Aqoxy2G03010' => 'aox', 'Aqoxy3G01158' => 'aox', 'Aqoxy3G03811' => 'aox', 'Aqoxy4G02342' => 'aox', 'Aqoxy5G03968' => 'aox', 'Aqoxy6G01684' => 'aox', 'Aqoxy7G03273' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2MM3YT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4DR6J6' => 'arhy', 'AT1G49360' => 'ath', 'AT1G57790' => 'ath', 'AT2G44735' => 'ath', 'AT3G18720' => 'ath', 'AT3G56470' => 'ath', 'AT4G00893' => 'ath', 'AT4G10660' => 'ath', 'AT4G10695' => 'ath', 'AT4G10700' => 'ath', 'AT4G12370' => 'ath', 'AT4G12382' => 'ath', 'ATR0706G108' => 'atr', 'ATR0706G176' => 'atr', 'ATR0706G284' => 'atr', 'ATR0851G001' => 'atr', 'Atru.chr13.1445' => 'acertr', 'Atru.chr13.1469' => 'acertr', 'Atru.chr2.1235' => 'acertr', 'Atru.chr2.342' => 'acertr', 'Atru.chr2.422' => 'acertr', 'Atru.chr2.424' => 'acertr', 'Atru.chr2.465' => 'acertr', 'Atru.chr2.481' => 'acertr', 'Atru.chr2.486' => 'acertr', 'Atru.chr2.488' => 'acertr', 'Atru.chr2.489' => 'acertr', 'Atru.chr5.110' => 'acertr', 'Atru.chr8.1486' => 'acertr', 'AUR62006191' => 'cqu', 'AUR62037031' => 'cqu', 'BcaB01g01708' => 'bca', 'BcaB01g01734' => 'bca', 'BcaB01g02647' => 'bca', 'BcaB01g02651' => 'bca', 'BcaB01g02678' => 'bca', 'BcaB01g02679' => 'bca', 'BcaB01g03228' => 'bca', 'BcaB02g08841' => 'bca', 'BcaB02g08843' => 'bca', 'BcaB02g08844' => 'bca', 'BcaB03g14398' => 'bca', 'BcaB03g16712' => 'bca', 'BcaB04g20176' => 'bca', 'BcaB05g22018' => 'bca', 'BcaB05g23747' => 'bca', 'BcaB05g23813' => 'bca', 'BcaB07g31732' => 'bca', 'BcaC01g02970' => 'bca', 'BcaC01g04596' => 'bca', 'BcaC01g04597' => 'bca', 'BcaC01g04623' => 'bca', 'BcaC02g12286' => 'bca', 'BcaC03g14450' => 'bca', 'BcaC03g16285' => 'bca', 'BcaC04g21189' => 'bca', 'BcaC04g23040' => 'bca', 'BcaC05g24302' => 'bca', 'BcaC07g39959' => 'bca', 'BcaC09g49525' => 'bca', 'BolC1t03516H' => 'bol', 'BolC2t08007H' => 'bol', 'BolC2t09692H' => 'bol', 'BolC2t10098H' => 'bol', 'BolC2t10171H' => 'bol', 'BolC3t15873H' => 'bol', 'BolC3t15900H' => 'bol', 'BolC3t18038H' => 'bol', 'BolC4t22191H' => 'bol', 'BolC5t29218H' => 'bol', 'BolC7t40718H' => 'bol', 'BolC7t40719H' => 'bol', 'BolC7t41000H' => 'bol', 'BolC7t41003H' => 'bol', 'BolC7t42933H' => 'bol', 'BolC8t50797H' => 'bol', 'BolC9t54170H' => 'bol', 'BolC9t56288H' => 'bol', 'BolC9t60041H' => 'bol', 'BraA01t02936Z' => 'bra', 'BraA02t06188Z' => 'bra', 'BraA02t07559Z' => 'bra', 'BraA02t07603Z' => 'bra', 'BraA03t12137Z' => 'bra', 'BraA03t12138Z' => 'bra', 'BraA03t12159Z' => 'bra', 'BraA03t12160Z' => 'bra', 'BraA07t27956Z' => 'bra', 'BraA07t29366Z' => 'bra', 'BraA09t36726Z' => 'bra', 'BraA09t38260Z' => 'bra', 'BraA09t38265Z' => 'bra', 'BraA09t38281Z' => 'bra', 'BraA09t41879Z' => 'bra', 'BraA10t42745Z' => 'bra', 'BraA10t42747Z' => 'bra', 'BraA10t45268Z' => 'bra', 'C01p35560' => 'bna', 'C02p18620' => 'bna', 'C02p40810' => 'bna', 'C02p41540' => 'bna', 'C03p35590' => 'bna', 'C03p35920' => 'bna', 'C03p57640' => 'bna', 'C04p05620' => 'bna', 'C05p04470' => 'bna', 'C07p03210' => 'bna', 'C07p03220' => 'bna', 'C07p05950' => 'bna', 'C07p24090' => 'bna', 'C08p31760' => 'bna', 'C09p12800' => 'bna', 'C09p34450' => 'bna', 'C09p73060' => 'bna', 'CAN.G397.56' => 'can', 'CANSAT64G2057' => 'cansat', 'CARHR036030' => 'chi', 'CARHR054340' => 'chi', 'CARHR054360' => 'chi', 'CARHR094100' => 'chi', 'CARHR094110' => 'chi', 'CARHR139790' => 'chi', 'CARHR166590' => 'chi', 'CARHR216300' => 'chi', 'CARHR253820' => 'chi', 'CARHR253830' => 'chi', 'CARHR253840' => 'chi', 'CARHR253850' => 'chi', 'CARHR253860' => 'chi', 'CARHR253870' => 'chi', 'Carub.0002s0673' => 'cru', 'Carub.0003s1850' => 'cru', 'Carub.0004s2747' => 'cru', 'Carub.0005s2324' => 'cru', 'Carub.0006s2964' => 'cru', 'Carub.0006s3151' => 'cru', 'Carub.0006s3152' => 'cru', 'Carub.0006s3153' => 'cru', 'Ca_00899_v3' => 'car', 'Ca_09011_v3' => 'car', 'Cc06_g05910' => 'ccan', 'Cfa007810' => 'cfa', 'Cfa007811' => 'cfa', 'Cfa009449' => 'cfa', 'Cfa009796' => 'cfa', 'Cfa013583' => 'cfa', 'Cfa016617' => 'cfa', 'Cfa016618' => 'cfa', 'Cfa021905' => 'cfa', 'Ciclev10003107m.g' => 'ccl', 'Ciclev10003216m.g' => 'ccl', 'Ciclev10003369m.g' => 'ccl', 'Ciclev10011976m.g' => 'ccl', 'Ciclev10027395m.g' => 'ccl', 'CiPaw.03G072100' => 'cil', 'CiPaw.10G010500' => 'cil', 'COL.COLO4_09711' => 'col', 'COL.COLO4_09712' => 'col', 'COL.COLO4_09720' => 'col', 'COL.COLO4_12645' => 'col', 'COL.COLO4_14626' => 'col', 'COL.COLO4_14629' => 'col', 'COL.COLO4_14639' => 'col', 'COL.COLO4_14641' => 'col', 'COL.COLO4_14643' => 'col', 'COL.COLO4_14644' => 'col', 'COL.COLO4_14733' => 'col', 'COL.COLO4_14754' => 'col', 'COL.COLO4_14832' => 'col', 'COL.COLO4_14877' => 'col', 'COL.COLO4_15278' => 'col', 'COL.COLO4_17685' => 'col', 'COL.COLO4_18753' => 'col', 'COL.COLO4_20081' => 'col', 'COL.COLO4_20290' => 'col', 'COL.COLO4_22245' => 'col', 'COL.COLO4_22259' => 'col', 'COL.COLO4_22267' => 'col', 'COL.COLO4_23032' => 'col', 'COL.COLO4_29476' => 'col', 'COL.COLO4_29491' => 'col', 'COL.COLO4_29718' => 'col', 'COL.COLO4_31189' => 'col', 'COL.COLO4_31632' => 'col', 'COL.COLO4_31677' => 'col', 'COL.COLO4_35199' => 'col', 'COL.COLO4_35200' => 'col', 'COL.COLO4_35245' => 'col', 'Cpa.g.sc5.10' => 'cpa', 'CSS0048691' => 'camsi', 'DCAR_020742' => 'dca', 'Dinv21199' => 'din', 'Dinv21700' => 'din', 'Dinv31694' => 'din', 'Dinv36205' => 'din', 'Dinv36214' => 'din', 'Duzib093G1514' => 'dzi', 'Duzib093G2076' => 'dzi', 'Duzib106G0631' => 'dzi', 'Duzib106G1385' => 'dzi', 'Duzib114G0876' => 'dzi', 'Duzib114G0895' => 'dzi', 'Duzib177G0059' => 'dzi', 'Duzib177G0518' => 'dzi', 'Duzib248G0416' => 'dzi', 'Duzib260G0007' => 'dzi', 'ECA236G4173' => 'eca', 'ECA248G0397' => 'eca', 'EL10Ac7g16907' => 'bvu', 'FAN02G2895' => 'fan', 'FAN05G3626' => 'fan', 'FAN14G2386' => 'fan', 'FAN14G4995' => 'fan', 'FvH4_6g18890' => 'fve', 'Glyma.03G196600' => 'gma', 'Glyma.10G073700' => 'gma', 'Glyma.13G154400' => 'gma', 'Glyma.19G194964' => 'gma', 'Gohir.A01G205800' => 'ghi', 'Gohir.A04G062200' => 'ghi', 'Gohir.A08G212150' => 'ghi', 'Gohir.D01G195200' => 'ghi', 'Gohir.D04G099000' => 'ghi', 'Gohir.D05G248150' => 'ghi', 'Gohir.D08G228850' => 'ghi', 'Gorai.002G239400' => 'gra', 'Gorai.004G243200' => 'gra', 'Gorai.009G259100' => 'gra', 'Gorai.009G401400' => 'gra', 'Gorai.013G207100' => 'gra', 'HanXRQChr01g0010051' => 'han', 'Haze_01392' => 'cav', 'Haze_09881' => 'cav', 'Haze_12502' => 'cav', 'Haze_14264' => 'cav', 'Haze_19622' => 'cav', 'Haze_19623' => 'cav', 'Hma1.2p1_0698F.1_g205490' => 'hma', 'HPP92_002127' => 'vpl', 'HPP92_002134' => 'vpl', 'HPP92_013708' => 'vpl', 'HPP92_026823' => 'vpl', 'HPP92_028691' => 'vpl', 'Hund03994' => 'sun', 'Lalb_Chr01g0018111' => 'lal', 'Lalb_Chr06g0172391' => 'lal', 'Lj3P997T36' => 'lonja', 'Lj5g0005331' => 'lja', 'Lsat_1_v5_gn_5_165000' => 'lsa', 'Lsat_1_v5_gn_8_77420' => 'lsa', 'Manes.08G026100' => 'mes', 'Manes.09G054600' => 'mes', 'MBI14_g22986_MAGBIO' => 'mbi', 'MBI19_g06975_MAGBIO' => 'mbi', 'MBI19_g10180_MAGBIO' => 'mbi', 'MBI19_g34546_MAGBIO' => 'mbi', 'MBI19_g37418_MAGBIO' => 'mbi', 'MBI19_g39778_MAGBIO' => 'mbi', 'MBI19_g39779_MAGBIO' => 'mbi', 'MBI19_g39962_MAGBIO' => 'mbi', 'MD12G1025100' => 'mdo', 'MD14G1023800' => 'mdo', 'Medtr1g059840' => 'mtr', 'Medtr2g020080' => 'mtr', 'Medtr7g104760' => 'mtr', 'Medtr7g104785' => 'mtr', 'Medtr7g104790' => 'mtr', 'Migut.C01006' => 'egut', 'Migut.C01036' => 'egut', 'Migut.J01025' => 'egut', 'Migut.L00995' => 'egut', 'Migut.O00798' => 'egut', 'MSTRG.10371' => 'ama', 'MSTRG.19268' => 'ama', 'MSTRG.26636' => 'ama', 'Nitab4.5_0000692g0040' => 'nta', 'Nn1g05876' => 'nnu', 'Nn2g13245' => 'nnu', 'Nn5g27741' => 'nnu', 'Nn7g36296' => 'nnu', 'Nn7g38181' => 'nnu', 'Oeu025671.3' => 'oeu', 'Oeu047204.1' => 'oeu', 'Oeu047860.1' => 'oeu', 'Peaxi162Scf00003g03416' => 'pax', 'Peaxi162Scf00003g03511' => 'pax', 'Peaxi162Scf00404g00218' => 'pax', 'Peaxi162Scf01233g00009' => 'pax', 'PGR142G0506' => 'pgr', 'PGR142G1600' => 'pgr', 'PGSC0003DMG400008951' => 'stu', 'Phvul.001G190800' => 'pvu', 'Potri.006G198901' => 'ptr', 'Potri.006G212600' => 'ptr', 'Potri.012G106800' => 'ptr', 'Potri.016G079300' => 'ptr', 'Prupe.7G109000' => 'ppe', 'Prupe.8G252900' => 'ppe', 'Psat3g032400' => 'psa', 'Psat3g032440' => 'psa', 'Psat6g080440' => 'psa', 'PSO017G2999' => 'pso', 'PSO063G0338' => 'pso', 'PSO210G0943' => 'pso', 'PSO210G1288' => 'pso', 'PSO210G3459' => 'pso', 'PSO210G6800' => 'pso', 'PSO541G2264' => 'pso', 'PSO832G3168' => 'pso', 'QL02p058170' => 'qlo', 'QL02p058175' => 'qlo', 'QL02p058185' => 'qlo', 'QL03p004509' => 'qlo', 'QL04p032678' => 'qlo', 'QL04p042600' => 'qlo', 'QL04p042652' => 'qlo', 'QL04p042669' => 'qlo', 'QL04p042854' => 'qlo', 'QL07p038675' => 'qlo', 'QL07p041255' => 'qlo', 'QL07p041329' => 'qlo', 'QL93p0100_0562' => 'qlo', 'QL93p0100_0576' => 'qlo', 'QL93p0100_0597' => 'qlo', 'RcHm_v2.0_Chr3g0473881' => 'rch', 'Rhsim01G0008500' => 'rsi', 'Rhsim01G0011000' => 'rsi', 'Rhsim01G0011200' => 'rsi', 'Rhsim01G0011400' => 'rsi', 'Rhsim01G0011500' => 'rsi', 'Rhsim01G0011600' => 'rsi', 'Rhsim01G0035900' => 'rsi', 'Rhsim01G0045800' => 'rsi', 'Rhsim03G0112600' => 'rsi', 'Rhsim08G0204600' => 'rsi', 'Rhsim08G0205000' => 'rsi', 'Rhsim08G0205300' => 'rsi', 'Rhsim10G0179200' => 'rsi', 'RhsimUnG0079600' => 'rsi', 'Sabra06G0163600' => 'sbr', 'Sabra16G0085000' => 'sbr', 'Sabra16G0087200' => 'sbr', 'Sabra19G0121800' => 'sbr', 'SalBow3G0903' => 'sbo', 'SalBow5G2315' => 'sbo', 'SalBow5G5642' => 'sbo', 'Sc20g0006330' => 'sci', 'SGA_v2.0_scaffold184G39968' => 'sas', 'SGA_v2.0_scaffold24G10323' => 'sas', 'SGA_v2.0_scaffold24G10329' => 'sas', 'SGA_v2.0_scaffold24G10400' => 'sas', 'SGA_v2.0_scaffold31G12907' => 'sas', 'SGA_v2.0_scaffold35G14063' => 'sas', 'SGA_v2.0_scaffold52G18942' => 'sas', 'Solyc02g069900.1' => 'sly', 'Solyc09g009880.3' => 'sly', 'Sopen02g019040' => 'spe', 'Sopen09g004630' => 'spe', 'Sp2g05780' => 'spa', 'Sp3g32580' => 'spa', 'Sp3g32590' => 'spa', 'Sp4g03050' => 'spa', 'Sp5g06085' => 'spa', 'Sp6g05180' => 'spa', 'Sp6g05200' => 'spa', 'Sp6g05210' => 'spa', 'Sp6g05220' => 'spa', 'Sp6g05700' => 'spa', 'Sp6g05710' => 'spa', 'Sp6g12720' => 'spa', 'Sp7g03220' => 'spa', 'TAR362G0940' => 'tar', 'TAR369G0060' => 'tar', 'TAR369G0559' => 'tar', 'TAR369G0746' => 'tar', 'TAR374G0175' => 'tar', 'TAR374G0203' => 'tar', 'TAR374G1264' => 'tar', 'TAR376G0082' => 'tar', 'TAR376G0134' => 'tar', 'TAR376G1075' => 'tar', 'TAR376G1185' => 'tar', 'TAR383G0168' => 'tar', 'TAR627G0263' => 'tar', 'TAR628G0017' => 'tar', 'TAR628G1131' => 'tar', 'TAR633G0845' => 'tar', 'TAR636G0708' => 'tar', 'TAR636G0782' => 'tar', 'TAR636G1022' => 'tar', 'TAR636G1931' => 'tar', 'TAR636G2415' => 'tar', 'TAR636G2462' => 'tar', 'TAR636G2857' => 'tar', 'TAR636G3010' => 'tar', 'TAR636G3207' => 'tar', 'TAR636G3329' => 'tar', 'TAR636G3669' => 'tar', 'TAR636G3684' => 'tar', 'THA.LOC104816392' => 'tha', 'THA.LOC104816671' => 'tha', 'Thecc.03G255600' => 'tca', 'Thecc.05G090300' => 'tca', 'Thecc.05G212700' => 'tca', 'Thecc.05G234700' => 'tca', 'Thecc.05G240100' => 'tca', 'Thecc.07G027300' => 'tca', 'Thecc.07G029900' => 'tca', 'Thecc.07G030000' => 'tca', 'Thhalv10002259m.g' => 'esa', 'Thhalv10006319m.g' => 'esa', 'Thhalv10006387m.g' => 'esa', 'Thhalv10015924m.g' => 'esa', 'Thhalv10022459m.g' => 'esa', 'Thhalv10023551m.g' => 'esa', 'Thhalv10027612m.g' => 'esa', 'Thhalv10028097m.g' => 'esa', 'Thhalv10028157m.g' => 'esa', 'Thhalv10028173m.g' => 'esa', 'Thhalv10028260m.g' => 'esa', 'Thhalv10028277m.g' => 'esa', 'Thhalv10029151m.g' => 'esa', 'Thhalv10029362m.g' => 'esa', 'Thhalv10029466m.g' => 'esa', 'Thhalv10029531m.g' => 'esa', 'Thhalv10029532m.g' => 'esa', 'TPR.G23322' => 'tpr', 'TPR.G23337' => 'tpr', 'TPR.G9893' => 'tpr', 'TWI12G1091' => 'twi', 'TWI39G1174' => 'twi', 'TWI39G1245' => 'twi', 'TWI56G0904' => 'twi', 'TWI63G1693' => 'twi', 'TWI75G0611' => 'twi', 'TWI77G1030' => 'twi', 'unitig_744.g24700' => 'ugi', 'vmacro19720' => 'vma', 'VMungo1383G3108' => 'vmu' ) $gf_id = 'HOM05D001286' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001286' ) $data_identifier = 'HOM05D001286' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 35, 'aar' => (int) 7, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 8, 'aox' => (int) 10, 'arhy' => (int) 2, 'ath' => (int) 11, 'atr' => (int) 4, 'acertr' => (int) 13, 'cqu' => (int) 2, 'bca' => (int) 29, 'bol' => (int) 19, 'bra' => (int) 18, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 14, 'cru' => (int) 8, 'car' => (int) 2, 'ccan' => (int) 1, 'cfa' => (int) 8, 'ccl' => (int) 5, 'cil' => (int) 2, 'col' => (int) 32, 'cpa' => (int) 1, 'camsi' => (int) 1, 'dca' => (int) 1, 'din' => (int) 5, 'dzi' => (int) 10, 'eca' => (int) 2, 'bvu' => (int) 1, 'fan' => (int) 4, 'fve' => (int) 1, 'gma' => (int) 4, 'ghi' => (int) 7, 'gra' => (int) 5, 'han' => (int) 1, 'cav' => (int) 6, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 1, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 1, 'lsa' => (int) 2, 'mes' => (int) 2, 'mbi' => (int) 8, 'mdo' => (int) 2, 'mtr' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 1, 'nnu' => (int) 5, 'oeu' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 15, 'rch' => (int) 1, 'rsi' => (int) 14, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 13, 'tar' => (int) 28, 'tha' => (int) 2, 'tca' => (int) 8, 'esa' => (int) 17, 'tpr' => (int) 3, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 1, 'vmu' => (int) 1 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1383G3108' $species_info = array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ) $local_species = 'vmu' $disabled = '' $selected = '' $num_hits = (int) 1